tractogram_removeinvalid
Remove invalid streamlines from a single or multiple tractograms/bundles.
Keywords : Invalid, Tractograms, Streamlines
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(tractogram)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | True | |
| tractogram | file | Tractogram or list of tractograms from which to remove invalid streamlines. | True | *.{trk,tck} |
Outputs
Section titled “Outputs”tractograms
Section titled “tractograms”Format : tuple val(meta), path(*.{trk,tck})
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | True | |
| *.{trk,tck} | file | Tractogram without invalid streamlines | True | *.{trk,tck} |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
Arguments (see process.ext)
Section titled “Arguments (see process.ext)”| Type | Description | Default | Choices | |
|---|---|---|---|---|
| cut_invalid | boolean | Cut invalid streamlines rather than removing them. Keep the longest segment only. | False | |
| remove_single_point | boolean | Consider single point streamlines as invalid. | False | |
| remove_overlapping_points | boolean | Consider streamlines with overlapping points as invalid. | False | |
| threshold | float | Maximum distance between two points to be considered overlapping. | 0.001 mm | |
| no_empty | boolean | Do not save empty tractogram. | False |
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2025-10-30